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In 1906 the Great Western Railway (GWR) constructed the Chalfont Viaduct to carry trains between London and High Wycombe across the river. In the mid-1980s, when the M25 was being constructed, the Misbourne was diverted under the motorway via underground concrete culverts. The route of the motorway was then aligned to pass through the arches of the Chalfont Viaduct.[1][2]

The Misbourne has for some years had intermittently reduced or stopped flow because of abstraction for supply from the aquifers feeding it. The low flow caused its course to be neglected or partially obstructed, so when the water companies undertook remedial measures which restored the flow, there were episodes of flooding in Chalfont St Peter and Chalfont St Giles village centres. Later work has restored the integrity of the course, and floods have not occurred since then.

The river is a 'perch' stream, flowing over a bed of impermeable material on top of a porous substrate. This state is only quasi-stable, since in periods of low rainfall the water table drops below the level of the impermeable layer. If ground works are then carried out which damage this layer, the river can sink into the porous substrate and disappear.

The upper part of the river was dry for over 3 years starting in November 2003 but re-appeared in February 2007 following several months of above-average rainfall which raised the water table.[3]